[English] 日本語
Yorodumi
- PDB-6vil: Crystal structure of mouse BAHCC1 BAH domain in complex with H3K27me3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vil
TitleCrystal structure of mouse BAHCC1 BAH domain in complex with H3K27me3
Components
  • BAH and coiled-coil domain-containing protein 1
  • Histone H3.1Histone H3
KeywordsSTRUCTURAL PROTEIN
Function / homology
Function and homology information


Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) ...Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / chromatin binding / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus
Similarity search - Function
Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain / BAH domain profile. / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 ...Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain / BAH domain profile. / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
Histone H3.1 / BAH and coiled-coil domain-containing protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.301 Å
AuthorsSong, J. / Lu, J.
CitationJournal: Nat.Genet. / Year: 2020
Title: BAHCC1 binds H3K27me3 via a conserved BAH module to mediate gene silencing and oncogenesis.
Authors: Fan, H. / Lu, J. / Guo, Y. / Li, D. / Zhang, Z.M. / Tsai, Y.H. / Pi, W.C. / Ahn, J.H. / Gong, W. / Xiang, Y. / Allison, D.F. / Geng, H. / He, S. / Diao, Y. / Chen, W.Y. / Strahl, B.D. / Cai, ...Authors: Fan, H. / Lu, J. / Guo, Y. / Li, D. / Zhang, Z.M. / Tsai, Y.H. / Pi, W.C. / Ahn, J.H. / Gong, W. / Xiang, Y. / Allison, D.F. / Geng, H. / He, S. / Diao, Y. / Chen, W.Y. / Strahl, B.D. / Cai, L. / Song, J. / Wang, G.G.
History
DepositionJan 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Derived calculations / Category: pdbx_struct_assembly / pdbx_struct_assembly_gen
Revision 1.2Nov 11, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Nov 18, 2020Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Dec 16, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.5Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BAH and coiled-coil domain-containing protein 1
B: BAH and coiled-coil domain-containing protein 1
I: Histone H3.1
J: Histone H3.1
D: BAH and coiled-coil domain-containing protein 1
E: BAH and coiled-coil domain-containing protein 1
F: BAH and coiled-coil domain-containing protein 1
G: BAH and coiled-coil domain-containing protein 1
H: BAH and coiled-coil domain-containing protein 1
C: BAH and coiled-coil domain-containing protein 1
L: Histone H3.1
M: Histone H3.1


Theoretical massNumber of molelcules
Total (without water)154,15612
Polymers154,15612
Non-polymers00
Water0
1
A: BAH and coiled-coil domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)18,5391
Polymers18,5391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BAH and coiled-coil domain-containing protein 1
J: Histone H3.1


Theoretical massNumber of molelcules
Total (without water)20,0002
Polymers20,0002
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: Histone H3.1
C: BAH and coiled-coil domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)20,0002
Polymers20,0002
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: BAH and coiled-coil domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)18,5391
Polymers18,5391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: BAH and coiled-coil domain-containing protein 1
L: Histone H3.1


Theoretical massNumber of molelcules
Total (without water)20,0002
Polymers20,0002
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: BAH and coiled-coil domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)18,5391
Polymers18,5391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: BAH and coiled-coil domain-containing protein 1
M: Histone H3.1


Theoretical massNumber of molelcules
Total (without water)20,0002
Polymers20,0002
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: BAH and coiled-coil domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)18,5391
Polymers18,5391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)184.176, 184.176, 70.276
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

-
Components

#1: Protein
BAH and coiled-coil domain-containing protein 1


Mass: 18539.135 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bahcc1, Kiaa1447 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q3UHR0
#2: Protein/peptide
Histone H3.1 / Histone H3


Mass: 1460.699 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.46 Å3/Da / Density % sol: 72.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.4 / Details: 1.6-1.8 M NaH2PO4/K2HPO4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 40066 / % possible obs: 99.9 % / Redundancy: 4 % / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.107 / Rrim(I) all: 0.218 / Χ2: 0.531 / Net I/σ(I): 3.2 / Num. measured all: 162176
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.3-3.4241.35439950.2970.7661.5590.501100
3.42-3.554.10.95440040.5120.5281.0920.497100
3.55-3.724.10.63640260.7530.3550.730.51199.5
3.72-3.914.10.40840080.8660.230.4690.509100
3.91-4.163.80.26939880.930.1590.3130.512100
4.16-4.483.90.15440300.9720.0890.1780.538100
4.48-4.934.20.13139980.9830.0720.150.528100
4.93-5.644.10.11839840.9850.0660.1350.532100
5.64-7.13.90.10440250.9870.0610.1210.545100
7.1-504.10.04740080.9980.0260.0540.634100

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DOV

4dov


Resolution: 3.301→46.044 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 29.33
RfactorNum. reflection% reflection
Rfree0.2828 2016 5.04 %
Rwork0.2479 --
obs0.2497 40020 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 196.08 Å2 / Biso mean: 93.7795 Å2 / Biso min: 41.3 Å2
Refinement stepCycle: final / Resolution: 3.301→46.044 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9381 0 0 0 9381
Num. residues----1245
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.301-3.38310.38891380.35132701100
3.3831-3.47450.37191560.32842741100
3.4745-3.57670.36341400.32352706100
3.5767-3.69210.34221420.30742703100
3.6921-3.8240.31141380.27632718100
3.824-3.9770.28091460.24722707100
3.977-4.15790.28641490.24032729100
4.1579-4.3770.24511490.21122744100
4.377-4.6510.28521440.20052698100
4.651-5.00970.25961400.2132719100
5.0097-5.51310.2611400.21842730100
5.5131-6.30910.31321480.24142696100
6.3091-7.94210.27371350.25932734100
7.9421-46.0440.22231510.2465267899
Refinement TLS params.Method: refined / Origin x: 48.9578 Å / Origin y: -21.0584 Å / Origin z: -11.1408 Å
111213212223313233
T0.3207 Å20.1868 Å2-0.0361 Å2-0.7006 Å20.0063 Å2--0.559 Å2
L0.6618 °2-0.2291 °2-0.3335 °2-0.3655 °20.0571 °2--1.691 °2
S0.0318 Å °0.1854 Å °-0.0143 Å °0.0597 Å °-0.0818 Å °-0.0149 Å °-0.2043 Å °0.1419 Å °0.0464 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2486 - 2642
2X-RAY DIFFRACTION1allB2486 - 2641
3X-RAY DIFFRACTION1allI22 - 33
4X-RAY DIFFRACTION1allJ22 - 33
5X-RAY DIFFRACTION1allD2485 - 2642
6X-RAY DIFFRACTION1allE2485 - 2642
7X-RAY DIFFRACTION1allF2487 - 2642
8X-RAY DIFFRACTION1allG2485 - 2642
9X-RAY DIFFRACTION1allH2485 - 2642
10X-RAY DIFFRACTION1allC2485 - 2642
11X-RAY DIFFRACTION1allL25 - 29
12X-RAY DIFFRACTION1allM25 - 28

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more